You may have an effect that doesn't do Alpha processing or messed up layer switches for retaining transparency and blending modes on a fully opaque source or something like that.... Impossible to know without actualyl seeing your project structure.
I can't get a text layer with three four letter words to render with a transparent layer. I've tried everything except changing the font, or calling PGE and demanding 50Hz power.
thanks for the clarity and specificity of "messed up layer switches", that's the type of incredibly insightful focused feedback that will help me solve my problem sometime this century ;-)
And sadly changing the font did not help. I think I'll sacrifice a chicken next...
Well, the chicken sacrifice did not work, although I am sure that makes Colonel Sanders sleep better.
It seems the problem was duplicated Pr plug ins in the common folder. Of course Pr had no problem with them, Ae not so much. Even though they were not Ae plug ins. And I don't use them in Pr. And they have nothing to do with transparency. Not corrupted plug ins, but two of the same plug ins. Dangerous stuff that is, having two of the same thing on our computers. Robustness defined, again, well done Adobe.
As an engineer with a handful of patents I can say this makes about as much sense as my car misfiring because I put an oversize coffee in the cupholder. Of my other car.